Calcium in PDB 6qhj: High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain

The structure of High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain, PDB code: 6qhj was solved by M.F.Pronker, H.G.Van Den Hoek, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.73 / 1.25
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.794, 79.631, 111.719, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 14.1

The structure of High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain (pdb code 6qhj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain, PDB code: 6qhj:

Calcium binding site 1 out of 1 in the High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:7.4 occ:1.00 OD1 A:ASP453 2.3 8.4 1.0 O A:ALA405 2.3 8.6 1.0 O A:LEU452 2.3 7.2 1.0 OD2 A:ASP356 2.3 7.6 1.0 OE1 A:GLU404 2.4 9.5 1.0 O A:HOH628 2.4 8.0 1.0 CG A:ASP453 3.3 9.0 1.0 CG A:ASP356 3.3 7.6 1.0 H A:ALA405 3.3 9.6 1.0 CD A:GLU404 3.3 8.9 1.0 HE1 A:MET358 3.4 13.6 1.0 C A:LEU452 3.4 7.5 1.0 OD1 A:ASP356 3.5 8.3 1.0 C A:ALA405 3.5 7.6 1.0 HA A:ASP453 3.5 9.5 1.0 H A:LEU452 3.6 9.2 0.2 H A:LEU452 3.6 9.2 0.8 OE2 A:GLU404 3.6 9.5 1.0 HE2 A:MET358 3.6 13.6 1.0 HH A:TYR347 3.6 11.1 1.0 HB3 A:PHE406 3.9 11.0 1.0 CE A:MET358 4.0 11.4 1.0 OD2 A:ASP453 4.0 11.3 1.0 HA A:PHE406 4.0 10.4 1.0 N A:ALA405 4.1 8.0 1.0 CA A:ASP453 4.1 8.0 1.0 HE2 A:TYR347 4.1 9.2 1.0 N A:ASP453 4.2 7.7 1.0 OH A:TYR347 4.2 9.2 1.0 CB A:ASP453 4.2 9.1 1.0 HB3 A:LEU452 4.2 10.2 1.0 N A:LEU452 4.3 7.7 1.0 CA A:LEU452 4.4 8.1 1.0 CA A:ALA405 4.4 8.0 1.0 HB3 A:GLU404 4.4 9.4 1.0 N A:PHE406 4.5 8.3 1.0 NA A:NA506 4.5 9.6 1.0 CA A:PHE406 4.5 8.7 1.0 HB2 A:ASP453 4.6 10.9 1.0 CB A:ASP356 4.6 7.2 1.0 CB A:PHE406 4.7 9.1 1.0 CG A:GLU404 4.7 8.6 1.0 O A:HOH667 4.7 8.8 1.0 HE3 A:MET358 4.7 13.6 1.0 CE2 A:TYR347 4.7 7.6 1.0 HB3 A:MET358 4.7 11.8 1.0 O A:HOH726 4.8 10.5 1.0 HB3 A:ASP356 4.8 8.7 1.0 HB3 A:ALA405 4.8 11.1 1.0 HB2 A:ASP356 4.9 8.7 1.0 CZ A:TYR347 4.9 7.6 1.0 CB A:LEU452 4.9 8.5 1.0 SD A:MET358 5.0 10.4 1.0 H A:ASP453 5.0 9.2 1.0 HB3 A:ASP453 5.0 10.9 1.0

M.F.Pronker, H.Van Den Hoek, B.J.C.Janssen. Design and Structural Characterisation of Olfactomedin-1 Variants As Tools For Functional Studies. Bmc Mol Cell Biol V. 20 50 2019.
ISSN: ISSN 2661-8850
PubMed: 31726976
DOI: 10.1186/S12860-019-0232-1